Hi, yes, indeed, when I originally send the inquiry about the derives_from, I was (not explicitly) also wondering about a adequate definition for a relationship which will connect and organism and a protein .The name in fact is just a label (although it needs to be quite well chosen). As Chris mentioned, 'extracted_from' and 'isolated_from' have some scope limitations. Anyway, there are some efforts in our group in extending RO (as I told Matthias in Dagsthul) for exploiting some reasoning capabilities (while composing several relationships for instance), we will come back to this later once it is in a good shape. For the moment, we will brainstorm a little bit more on 'derives_from' and put it on your consideration. cheers, Erick Dr. Mathias Brochhausen wrote:
Hi, Erick, hi Chris,
I completely agree with Chris. The most important thing is the formal definition of the relation. Stick a name to it is more or less arbitrary. The problem with derives_from was mainly that it was unclear whether there really are derives_from relations of the continuation type. I think they do not exist. We have merely cases of fission and fusion. The list of alternatives you give hints that maybe there might be a misuse of derives_from, but that should be checked case by case.
Best, Mathias
Chris Mungall schrieb:
I would first define the relation you want, then decide on the name.
extracted_from and isolated_from appears incorrect, unless you want to scope your ontology to describing only proteins extracted in experiments.
It would seem that a protein may not fit the criteria of a biologically significant amount of matter of a whole organism. In fact, in an example somewhat analagous to Mathia's, there may be no continuation of matter in the case of viruses.
depending on your definition of "encoded_by" and a more rigid definition of SO:gene, it may be sufficient to represent the partonomic relations between genes and organisms.
you can request relations on the ro tracker obofoundry.org/ro
btw, http://www.cellcycleontology.org/ontology/cco.owl is a dead link
On Aug 14, 2007, at 5:39 AM, Erick Antezana wrote:
Dear all,
currently, our proteins in CCO are linked to their respective organisms by using the relationship "derives_from"; however, as Mathias makes references in one of his articles [1], this relationship should be carefully chosen and it seems that CCO is misusing it. In that sense, we were wondering whether another relationship could be proposed? such as:
extracted_from? comes_from? occurs_in? isolated_from? appears_in_organism?
cheers, Erick
[1] http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf
--================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM erant@psb.ugent.be http://www.psb.ugent.be/~erant ==================================================================
_______________________________________________ ccofriends mailing list ccofriends@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/ccofriends
-- ================================================================== Erick Antezana http://www.cellcycleontology.org PhD student Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM erant@psb.ugent.be http://www.psb.ugent.be/~erant ==================================================================